Dataset Information

MiRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.

ABSTRACT: MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up- and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA-target interaction databases. The updated version of miRTarBase is now available at http://miRTarBase.cuhk.edu.cn/.

SUBMITTER: Huang HY

PROVIDER: S-EPMC7145596 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.

Huang Hsi-Yuan HY Lin Yang-Chi-Dung YC Li Jing J Huang Kai-Yao KY Shrestha Sirjana S Hong Hsiao-Chin HC Tang Yun Y Chen Yi-Gang YG Jin Chen-Nan CN Yu Yuan Y Xu Jia-Tong JT Li Yue-Ming YM Cai Xiao-Xuan XX Zhou Zhen-Yu ZY Chen Xiao-Hang XH Pei Yuan-Yuan YY Hu Liang L Su Jin-Jiang JJ Cui Shi-Dong SD Wang Fei F Xie Yue-Yang YY Ding Si-Yuan SY Luo Meng-Fan MF Chou Chih-Hung CH Chang Nai-Wen NW Chen Kai-Wen KW Cheng Yu-Hsiang YH Wan Xin-Hong XH Hsu Wen-Lian WL Lee Tzong-Yi TY Wei Feng-Xiang FX Huang Hsien-Da HD

Nucleic acids research 20200101 D1

MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorpo ...[more]

PMID: 31647101

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Project description:BackgroundDetermination of functional pathways regulated by microRNAs (miRNAs), while an essential step in developing therapeutics, is challenging. Some miRNAs have been studied extensively; others have limited information. In this study, we focus on 254 miRNAs previously identified as being associated with colorectal cancer and their database-identified validated target genes.MethodsWe use RNA-Seq data to evaluate messenger RNA (mRNA) expression for 157 subjects who also had miRNA expression data. In the replication phase of the study, we replicated associations between 254 miRNAs associated with colorectal cancer and mRNA expression of database-identified target genes in normal colonic mucosa. In the discovery phase of the study, we evaluated expression of 18 miR-NAs (those with 20 or fewer database-identified target genes along with miR-21-5p, miR-215-5p, and miR-124-3p which have more than 500 database-identified target genes) with expression of 17 434 mRNAs to identify new targets in colon tissue. Seed region matches between miRNA and newly identified targeted mRNA were used to help determine direct miRNA-mRNA associations.ResultsFrom the replication of the 121 miRNAs that had at least 1 database-identified target gene using mRNA expression methods, 97.9% were expressed in normal colonic mucosa. Of the 8622 target miRNA-mRNA associations identified in the database, 2658 (30.2%) were associated with gene expression in normal colonic mucosa after adjusting for multiple comparisons. Of the 133 miRNAs with database-identified target genes by non-mRNA expression methods, 97.2% were expressed in normal colonic mucosa. After adjustment for multiple comparisons, 2416 miRNA-mRNA associations remained significant (19.8%). Results from the discovery phase based on detailed examination of 18 miRNAs identified more than 80 000 miRNA-mRNA associations that had not previously linked to the miRNA. Of these miRNA-mRNA associations, 15.6% and 14.8% had seed matches for CRCh38 and CRCh37, respectively.ConclusionsOur data suggest that miRNA target gene databases are incomplete; pathways derived from these databases have similar deficiencies. Although we know a lot about several miRNAs, little is known about other miRNAs in terms of their targeted genes. We encourage others to use their data to continue to further identify and validate miRNA-targeted genes.

Dataset Information

MiRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.

Publications

miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.

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